Bologa Alexandru Marian, Stoica Ileana, Constantin Nicoleta Denisa, Ecovoiu Alexandru Al
Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania.
Insects. 2023 May 25;14(6):494. doi: 10.3390/insects14060494.
Natural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. (the fruit fly) is a eukaryotic model organism with NTs standing for about 20% of its genome and has contributed significantly to the understanding of various aspects of transposon biology. Our study describes an accurate approach designed to map class II transposons (DNA transposons) in the genome of the Horezu_LaPeri fruit fly strain, consecutive to Oxford Nanopore Technology sequencing. A whole genome bioinformatics analysis was conducted using Genome ARTIST_v2, LoRTE and RepeatMasker tools to identify DNA transposons insertions. Then, a gene ontology enrichment analysis was performed in order to evaluate the potential adaptive role of some DNA transposons insertions. Herein, we describe DNA transposon insertions specific for the Horezu_LaPeri genome and a predictive functional analysis of some insertional alleles. The PCR validation of P-element insertions specific for this fruit fly strain, along with a putative consensus sequence for the KP element, is also reported. Overall, the genome of the Horezu_LaPeri strain contains several insertions of DNA transposons associated with genes known to be involved in adaptive processes. For some of these genes, insertional alleles obtained via mobilization of the artificial transposons were previously reported. This is a very alluring aspect, as it suggests that insertional mutagenesis experiments conducting adaptive predictions for laboratory strains may be confirmed by mirroring insertions which are expected to be found at least in some natural fruit fly strains.
天然转座子（NTs）是在原核生物和真核生物基因组中均能发现的可移动DNA序列。（果蝇）是一种真核模式生物，其基因组中转座子约占20%，对转座子生物学各个方面的理解有重要贡献。我们的研究描述了一种精确方法，该方法用于在Horezu_LaPeri果蝇品系基因组中定位II类转座子（DNA转座子），该方法是在牛津纳米孔技术测序之后进行的。使用Genome ARTIST_v2、LoRTE和RepeatMasker工具进行了全基因组生物信息学分析，以识别DNA转座子插入。然后，进行了基因本体富集分析，以评估某些DNA转座子插入的潜在适应性作用。在此，我们描述了Horezu_LaPeri基因组特有的DNA转座子插入以及一些插入等位基因的预测功能分析。还报道了针对该果蝇品系的P元件插入的PCR验证以及KP元件的推定共有序列。总体而言，Horezu_LaPeri品系的基因组包含与已知参与适应性过程的基因相关的多个DNA转座子插入。对于其中一些基因，先前已报道了通过人工转座子动员获得的插入等位基因。这是一个非常诱人的方面，因为这表明对实验室品系进行适应性预测的插入诱变实验可能通过反映至少在一些天然果蝇品系中预期会发现的插入来得到证实。
